More American children than previously thought may be suffering from neurological damage because their mothers drank alcohol during pregnancy, according to a new study.

The study, published Tuesday in the journal JAMA, estimates that fetal alcohol syndrome and other alcohol-related disorders among American children are at least as common as autism. The disorders can cause cognitive, behavioral and physical problems that hurt children’s development and learning ability.

The researchers evaluated about 3,000 children in schools in four communities across the United States and interviewed many of their mothers. Based on their findings, they estimated conservatively that fetal alcohol spectrum disorders affect 1.1 to 5 percent of children in the U.S., up to five times previous estimates. About 1.5 percent of children are currently diagnosed with autism.

“This is an equally common, or more common, disorder and one that’s completely preventable and one that we are missing,” said Christina Chambers, one of the study authors and a professor of pediatrics at the University of California, San Diego. “If it truly is affecting a substantial proportion of the population, then we can do something about it. We can provide better services for those kids, and we can do a better job of preventing the disorders to begin with.”

The range of fetal alcohol spectrum disorders (also called FASDs) can cause cognitive, behavioral and physical difficulties. The most severe is fetal alcohol syndrome, in which children have smaller-than-typical heads and bodies, as well as eyes unusually short in width, thin upper lips, and smoother-than-usual skin between the nose and mouth, Dr. Chambers said. A moderate form is partial fetal alcohol syndrome. Less severe is alcohol-related neurodevelopmental disorder, in which children have neurological but not physical characteristics and it is known that their mothers drank during pregnancy.

It has been unclear how common these disorders are because the facial features are subtle, and some effects, like problems paying attention or recognizing the consequences of behavior, can apply to other diagnoses. Also, the degree and area of a child’s brain damage appears to vary depending on when and how much during pregnancy the mother drank, as well as genetics, so symptoms can vary, too.

Then there is the stigma that often makes mothers reluctant to acknowledge alcohol consumption.

“When you identify a kid with FASD, you’ve just identified a mom who drank during pregnancy and harmed her child,” said Susan Astley, director of the Fetal Alcohol Syndrome Diagnostic and Prevention Network at the University of Washington, who was not involved in the study.

While Dr. Astley, a longtime expert in the field, said she admired the researchers’ hard work, she said the reliability of the study’s numbers was hampered by several factors. For example, only 60 percent of eligible families in the schools allowed their children to be evaluated and more than a third of those children’s mothers declined to answer questions about drinking during pregnancy.

“If we could generate accurate estimates of FASD, we’d all benefit,” Dr. Astley said. “But the major limitations in the study design render the results, for the most part, uninterpretable.”

The authors of the study, which was funded by the National Institute on Alcohol Abuse and Alcoholism, acknowledged the study’s limitations and tried to partly compensate by providing a conservative estimate (of 1.1 percent to 5 percent) that is likely low and another estimate (of 3.1 percent to 9.9 percent) that is likely high. Dr. Chambers also said the results might not generalize across the country because although the four communities were diverse, they did not include a large, high-poverty urban area or certain rural or indigenous communities that struggle with high rates of alcoholism.

The locations, which are not named in the publication, include small-to-midsize cities in the Midwest and Rocky Mountains, a Southeast county and a Pacific Coast city the authors identified in interviews as San Diego. Participating first graders were given neurodevelopmental evaluations and most also had their facial features evaluated by dysmorphologists. About 62 percent of the first graders’ mothers were interviewed.

Of 2,962 children evaluated, the researchers identified 222 with a fetal alcohol spectrum disorder, Dr. Chambers said. All but two of them had not been previously diagnosed, although the authors said many parents had been aware their children had learning and behavioral difficulties.

“It’s kind of like the hidden problem,” said Dr. Howard Taras, a study author and professor at the University of California, San Diego, who is the physician for the San Diego Unified School District, which participated in the study. “If not in one classroom, certainly in another, there’s going to be one or two kids with these problems, but they’re not identified as such.”

Identifying children with alcohol-related impairments can help teachers and psychologists work with them more effectively, experts said.

Even if educational approaches might resemble those for other special needs children, the diagnosis tells teachers behavior problems are “not because this child is disobedient, it’s because of some neurological disorder,” said Dr. Svetlana Popova, a senior scientist at the Centre for Addiction and Mental Health’s Institute for Mental Health Policy Research in Toronto, who was a co-author of an editorial about the new study.

Dr. Astley said a diagnosis might inform medical treatment, too, because some medications, like Ritalin, might work for inherited attention deficit disorder, but not attention deficit symptoms caused by alcohol.

Recently health authorities in the United States have sharpened warnings about alcohol in pregnancy. A 2015 American Academy of Pediatrics report said “no amount of alcohol intake should be considered safe” during any trimester. In 2016, the Centers for Disease Control and Prevention, noting that half of American pregnancies are unplanned, recommended that sexually active women who are not using birth control “not drink alcohol at all.”

To the astonishment of people working with alcohol-damaged children, the C.D.C. report unleashed a swirl of pushback from those who considered the advice insulting, shaming or over-the-top.

“People say, ‘Don’t be ridiculous, I went to a wine tasting and my kid came out fine,’” Dr. Taras said. “But the C.D.C. is saying, ‘We don’t know. Maybe you just won the lottery.’”

Dr. Popova said she hoped the new study would make people pay attention.

“Alcohol can damage every system of the body,” she said. “We have to scream about this problem to the world.”